GeneBe

rs5873543

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003085.5(SNCB):​c.282+49_282+62delACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 714,874 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000056 ( 0 hom. )

Consequence

SNCB
NM_003085.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.15

Publications

0 publications found
Variant links:
Genes affected
SNCB (HGNC:11140): (synuclein beta) This gene encodes a member of a small family of proteins that inhibit phospholipase D2 and may function in neuronal plasticity. The encoded protein is abundant in lesions of patients with Alzheimer disease. A mutation in this gene was found in individuals with dementia with Lewy bodies. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
SNCB Gene-Disease associations (from GenCC):
  • Lewy body dementia
    Inheritance: Unknown, AD Classification: MODERATE, LIMITED Submitted by: Genomics England PanelApp, Ambry Genetics

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003085.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SNCB
NM_003085.5
MANE Select
c.282+49_282+62delACACACACACACAC
intron
N/ANP_003076.1Q16143
SNCB
NM_001001502.3
c.282+49_282+62delACACACACACACAC
intron
N/ANP_001001502.1Q16143
SNCB
NM_001363140.2
c.282+49_282+62delACACACACACACAC
intron
N/ANP_001350069.1Q16143

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SNCB
ENST00000393693.7
TSL:1 MANE Select
c.282+49_282+62delACACACACACACAC
intron
N/AENSP00000377296.2Q16143
SNCB
ENST00000310112.7
TSL:1
c.282+49_282+62delACACACACACACAC
intron
N/AENSP00000308057.3Q16143
SNCB
ENST00000614675.4
TSL:1
c.240+49_240+62delACACACACACACAC
intron
N/AENSP00000479489.1G4Y816

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000560
AC:
4
AN:
714874
Hom.:
0
AF XY:
0.00000261
AC XY:
1
AN XY:
383280
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
19212
American (AMR)
AF:
0.00
AC:
0
AN:
43154
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21070
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34146
South Asian (SAS)
AF:
0.00
AC:
0
AN:
70694
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
47468
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2764
European-Non Finnish (NFE)
AF:
0.00000907
AC:
4
AN:
440914
Other (OTH)
AF:
0.00
AC:
0
AN:
35452
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.650
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs5873543; hg19: chr5-176053336; API